4JGP
The crystal structure of sporulation kinase D sensor domain from Bacillus subtilis subsp in complex with pyruvate at 2.0A resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 298 | 0.2 M AMMONIUM SULFATE, 0.1 M SODIUM CACODYLATE:HCL AND 30% (W/V) PEG 8000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.89 | 57.49 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 76.374 | α = 90 |
b = 82.151 | β = 90 |
c = 90.678 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 315r | MIRRORS | 2011-11-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-ID | APS | 19-ID |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym I (Observed) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | ||||||||
1 | 2.03 | 50 | 99.8 | 0.063 | 33.1 | 7.9 | 36578 | 23.8 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.03 | 2.07 | 100 | 0.638 | 4.9 | 7.9 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||||
X-RAY DIFFRACTION | SAD | 2.03 | 37.42 | 1.34 | 63152 | 3161 | 88.9 | 0.181 | 0.179 | 0.216 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
1.0188 | -1.6011 | 0.5823 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 14.892 |
f_angle_d | 1.043 |
f_chiral_restr | 0.07 |
f_bond_d | 0.007 |
f_plane_restr | 0.004 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3242 |
Nucleic Acid Atoms | |
Solvent Atoms | 298 |
Heterogen Atoms | 12 |
Software
Software | |
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Software Name | Purpose |
MLPHARE | phasing |
PHENIX | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |